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agplus: a rapid and flexible tool for aggregation plots.

Kazumitsu Maehara1, Yasuyuki Ohkawa1

  • 1Department of Advanced Medical Initiatives, JST-CREST, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.

Bioinformatics (Oxford, England)
|May 22, 2015
PubMed
Summary
This summary is machine-generated.

agplus is a command-line tool that generates data for aggregation plots in ChIP-Seq analysis. It allows flexible grouping of data based on regulatory regions or transcription initiation sites for better signal distribution evaluation.

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Area of Science:

  • Epigenetics
  • Genomics
  • Bioinformatics

Background:

  • ChIP-Seq data analysis frequently utilizes aggregation plots to assess signal distributions.
  • Defining specific genomic regions of interest is crucial for accurate interpretation.

Purpose of the Study:

  • To introduce agplus, a novel command-line tool for generating aggregation plot data.
  • To enable flexible and rapid creation of tailored text tables for aggregation plots.

Main Methods:

  • agplus is a command-line tool implemented in Ruby.
  • The software supports Linux and Mac OSX operating systems.
  • It facilitates the generation of text tables for aggregation plots.

Main Results:

  • agplus enables the creation of customized data tables for aggregation plots.
  • Users can define multiple groups based on specific criteria like regulatory regions or transcription initiation sites.
  • The tool provides a flexible and rapid method for data preparation.

Conclusions:

  • agplus simplifies and enhances the process of preparing data for ChIP-Seq aggregation plots.
  • The tool's flexibility allows for detailed analysis of signal distributions at user-defined genomic locations.